limorhyde (linear models for rhythmicity, design) enables differential analysis of circadian transcriptome data using state-of-the-art methods for differential expression.

For details about the method and to see how we used it to analyze circadian transcriptome data from various experimental designs, check out the paper and the accompanying results.

Installation

If you use RStudio, go to Tools -> Global Options… -> Packages -> Add… (under Secondary repositories), then enter:

You only have to do this once. Then you can install or update the package by entering:

if (!requireNamespace('BiocManager', quietly = TRUE))
  install.packages('BiocManager')

BiocManager::install('limorhyde')

Alternatively, you can install or update the package by entering:

if (!requireNamespace('BiocManager', quietly = TRUE))
  install.packages('BiocManager')

BiocManager::install('limorhyde', site_repository = 'https://hugheylab.github.io/drat/')

There’s also docker image, which has all dependencies installed.

Usage

For an introduction to the package, read the vignette. For more details, check out the reference documentation.